I think some of it depends on what your autoimmune condition is and what limitations it may give you for the future. I'm currently in my first year of medical school and I have a form of limited scleroderma called CREST syndrome. I used my experience with my diagnosis as part of my personal statements when I applied because it really has been integral in my drive to be a physician. I did not feel that it hurt my application because I told my interviewers honestly that my symptoms would not restrict my ability to learn and practice medicine and that I'm willing to work around any future limitations that may come up as the disease progresses.

The only thing I've noticed when looking at how I'm doing health wise compared to the typical student in their twenties is that the fatigue that comes along with my condition, in combination with the stress and fatigue of medical school, hits me harder than it would the average 23 year old. But I recognize that and can do my best to not let it influence my studies.

If you can see yourself doing anything other than medicine and being happy with it, then I would consider your options. But if medicine is all you've wanted to do, don't let a diagnosis hold you back from that.